Kyle I'm thinking this is a wiring harness issue or something with the computer. Since we talked last about this P0689 code, I haven't been able to get rid of it either after the 4R70W swap.
What was your original PCM code for that auto, mine was VDX1, we flashed a manual code from an exact year 2006 mustang GT to the computer and pulled the P0689 code right away. A couple of other issues too, the emissions would not set as the evap, cats and o2s would never complete cycle, the rear passenger reverse light would stay on all the time. I just pulled the bulb for the time being.
Figured we try having a Ford tech reflash the pcm with the IDS software so I could have the proper miles on my computer with the vin number matching hoping that would set the emissions but that didn't work either. Same P0689 code and no change in the emission status.
The last thing which concerns me is in my case when you start the car it runs open loop, then closes like it should, then opens back up and never closes again. Probably why it won't set emissions status.
Will tune it now in open loop as it's a bit rich, otherwise it runs fine, have logged 500 miles on it so far without any driving issues.
Lastly, after about 250 miles the P0689 and the P1000 did clear, but a P0351
Ignition coil A Cop-A Primary/secondary CK T appeared. I changed the plug and cop, checked with a noid light and everything seems to be working.
Cleared the DTC and after startup checked the DTC and wouldn't ya know it the P0689 code appeared again.
Will be following your thread here for sure.